I think I just found the problem. bin/config.php was not finding the apache.vhost.wikidot.conf file and couldn't update the variable names. I have fixed my script and am running another test install.

Sorry for being such a pest! I'm under some pressure at work to get a Wikidot install running on our internal network and have been testing like crazy at home to make sure it will work as well as your hosted site. I must be over 20 test installs now since you released Wikidot to the open source community.